Suspended Essendon coach James Hird has forced a humiliating backdown from the AFL and its chief executive Andrew Demetriou and will be fully paid while he sits out next season.

But much bigger problems loom for Essendon.

Former World Anti-Doping Agency (WADA) president John Fahey said it is only a matter of time before the Australian Sports Anti-Doping Authority (ASADA) issues infraction notices over Essendon's supplements scandal.

"I expect there will be several charges by ASADA. It's only a matter of when," Fahey said.

It is the first time an anti-doping official has confirmed publicly that charges are likely over the scandal.

In an interview with the Australian Financial Review published on Friday, Fahey did not indicate who was likely to be charged.

Late on Friday, Essendon and the AFL announced an astonishing settlement that represented a major win for Hird.

At issue was whether the club could pay Hird during his 12-month suspension for his involvement in Essendon's supplements program.

Essendon president Paul Little said it was only implied in the club's agreement with the AFL that Hird could not be paid next year.

So Essendon will not pay him any money in 2014, but will pay him his reported $1 million salary in advance before December 31.

The AFL said it accepted this arrangement.

But Demetriou was adamant last week that Essendon was not paying Hird while he is suspended.

"He is not permitted to be paid by the Essendon Football Club," Demetriou told Radio station 3AW.

It put the club in the middle of an increasingly bitter war between the Hird camp and the AFL, especially Demetriou.

Essendon and the AFL reach agreement over Hird's pay

"Whilst it is acknowledged that James Hird's pay wasn't dealt with in the formal deed of settlement between Essendon and the AFL, complex discussions relating to James Hird's legally enforceable employment contract have continued between the parties," Essendon president Paul Little said in a statement.

"It has been very difficult to have this matter adequately resolved whilst being played out in the public arena.

"To settle this impasse, Essendon has resolved that it will pay James Hird in advance to cover the 2014 year consistent with Hird's employment contract obligations.

"This also meets the implied terms of the deed of settlement.

"The implied terms of the AFL sanction indicate that James Hird cannot be paid for a 12 month period, therefore he will not be paid during the calendar period January 1 - December 31, 2014."

The AFL released a short statement confirming the agreement, in stark contrast to a lengthy media release on Thursday where Demetriou had threatened to withhold money from Essendon.

"The AFL has accepted Essendon's position that James Hird will not be paid in 2014, and equally the AFL have accepted that Essendon has the right to make payments to James Hird in the 2013 year as it sees fit," the league said.

Fahey also savaged Essendon in his media interview, saying WorkSafe Victoria should investigate the club over the supplements controversy and questioned how Hird can return as coach once his suspension ends.

He also derided the AFL as "a sacred cow".

Essendon have been under ASADA investigation since February, when the anti-doping body and the AFL announced a joint probe into the club's 2011-12 supplements program.

The AFL's investigation ended in late August, days before the finals, with a range of severe penalties that included a 12-month suspension for Hird.

But ASADA have given no indication on when they will make their findings.